title: Experimental evolution of pseudogenization and gene loss in a plant RNA virus.
abstract: Viruses have evolved highly streamlined genomes and a variety of mechanisms to compress them, suggesting that genome size is under strong selection. Horizontal gene transfer has, on the other hand, played an important role in virus evolution. However, evolution cannot integrate initially nonfunctional sequences into the viral genome if they are rapidly purged by selection. Here we report on the experimental evolution of pseudogenization in virus genomes using a plant RNA virus expressing a heterologous gene. When long 9-week passages were performed, the added gene was lost in all lineages, whereas viruses with large genomic deletions were fixed in only two out of ten 3-week lineages and none in 1-week lineages. Illumina next-generation sequencing revealed considerable convergent evolution in the 9- and 3-week lineages with genomic deletions. Genome size was correlated to within-host competitive fitness, although there was no correlation with virus accumulation or virulence. Within-host competitive fitness of the 3-week virus lineages without genomic deletions was higher than for the 1-week lineages. Our results show that the strength of selection for a reduced genome size and the rate of pseudogenization depend on demographic conditions. Moreover, for the 3-week passage condition, we observed increases in within-host fitness, whereas selection was not strong enough to quickly remove the nonfunctional heterologous gene. These results suggest a demographically determined "sweet spot" might exist, where heterologous insertions are not immediately lost while evolution can act to integrate them into the viral genome.
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain.
authors.forename: Mark P
authors.initials: MP
authors.lastname: Zwart
authors.forename: Anouk
authors.initials: A
authors.lastname: Willemsen
authors.forename: José-Antonio
authors.initials: JA
authors.lastname: Daròs
authors.forename: Santiago F
authors.initials: SF
authors.lastname: Elena
mesh_terms: D002874:Chromosome Mapping; D003001:Cloning, Molecular; D019143:Evolution, Molecular; D017353:Gene Deletion; D022761:Gene Transfer, Horizontal; D016679:Genome, Viral; D010942:Plant Viruses / Q000235:genetics* / Q000502:physiology; D020641:Polymorphism, Single Nucleotide; D011544:Pseudogenes; D012328:RNA Viruses / Q000235:genetics* / Q000502:physiology; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012641:Selection, Genetic; D014026:Nicotiana / Q000821:virology; D014779:Virus Replication
chemical_list: D012367:RNA, Viral
keywords: fitness; genome evolution; horizontal gene transfer; next-generation sequencing; plant virus; pseudogenization